I'm trying to use this HMM that I have with my installation of Anvio using just HMMER: https://github.com/merenlab/anvio/blob/master/anvio/data/hmm/Bacteria_71/genes.hmm.gz
I've went through the source code below but it's not very clear how it's running: https://github.com/merenlab/anvio/blob/master/bin/anvi-run-hmms
The only way I can get this to run is by gzipping, then pressing the HMM, and then using hmmscan. Is this the only way to run HMMER? I'm not sure if Anvio decompresses and presses the HMM each time it is running.
Also, if you're running a set of HMMs against the proteome of a single organism, should you use HMMSCAN or HMMSEARCH?